12
votes
Accepted
How do I figure out how many monomer configurations I need for my simulation?
tldr; it depends on flexibility / number of rotatable bonds
A while ago, I answered a related question - in general, molecules with fewer "rotatable bonds" need fewer conformers geometries ...
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9
votes
Accepted
Alternatives to VEDA 4 vibrational energy distribution analysis software?
LocVib (part of MoViPac)
I have never used VEDA before, but according to the paper, it decomposes the normal modes into vibrations of atomic groups, bond stretching, bending or something else. ...
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9
votes
Accepted
Exchange-Correlation Two-Electron Integrals
I assume you're referring to eq 51 of the Hirata-Head-Gordon-Bartlett paper.
One should note that these are not two-electron integrals, since there is only one spatial position; these are rather ...
- 20k
5
votes
What do the indices mean in an FCIDUMP file?
"I was able to guess most of results, except the ones with value
0.663472."
I am able to confirm that your integrals are correct even for the 0.663472 case, because by calculating them ...
5
votes
Accepted
What is the best way to save a psi4 molecule object in Python?
If you only need the geometry, molecular charge, and other related quantities, then h2_geometry.to_dict() is what you want. You can then save the returned ...
- 66
5
votes
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Computing analytic derivatives of molecular Hamiltonians obtained from solving Hartree-Fock equations
PySCF and Psi4 both implement analytical geometric Hessians for Hartree-Fock calculations. The computation of the geometric Hessian indeed requires solving the coupled perturbed Hartree-Fock equations:...
- 20k
5
votes
Accepted
Calculating first and second derivatives of a molecular Hamiltonian?
The derivatives of a molecular Hamiltonian with respect to nuclear coordinates can be performed analytically (as you correctly pointed out), and therefore does not need PySCF or Psi4, which are ...
5
votes
Accepted
Error running psi4 on charged molecules
As you already figured out, the error is that the charge and multiplicity are inconsistent with the molecule; this is what Psi4 tells you:
qcelemental.exceptions.ValidationError: Inconsistent or ...
- 20k
5
votes
How do I figure out how many monomer configurations I need for my simulation?
At a rough guess you can assume that the number of conformers you need to generate (N_conf) is directly proportional to the number of rotatable bonds (N_rot) in a given compound. I seem to recall that ...
4
votes
What do the indices mean in an FCIDUMP file?
I would like to post a partial answer that I have for now.
For the indices ijkl in the FCIDUMP file, it corresponds to the integral (see https://theochem.github.io/horton/2.0.2/user_hamiltonian_io....
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4
votes
Psi4 Takes too Long to Save Computation Results to Python Notebook
I ran the calculation for ethanol and it took me 0.78 mins.
System Specs:
...
- 3,145
4
votes
Accepted
Decay rate of DSD-PBEPBE-D3BJ
I guess the OP is referring to the asymptotic potential which is -1/r with the optimized effective potential (OEP) but which decays exponentially with density functionals as well as Hartree-Fock ...
- 20k
2
votes
PSI4 SAPT calculation: failure to write
I suspect it turned out to be an issue with scratch space. I moved the scratch location to a local compute node instead of a networked filesystem scratch space. The variable to be set up is $...
- 233
2
votes
Accepted
Psi4 functionnals: LDA0
As Tyberius already stated in a comment above, LDA0 is a hybrid functional. However, you can't even expect two different LDAs to give the same results! SVWN5 is different from SVWN3 is different from ...
- 20k
2
votes
Accepted
How do I install the beta5 version of PSI4 on my WebMO Basic server?
I then tried to compute the energy of hexaiodostannate(IV) at the wB97X-2(TQZ)/def2-TZVPPD level of theory
wB97X-2(TQZ), published by Chai and Head-Gordon in doi:10.1063/1.3244209 is a double hybrid ...
- 20k
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